Locus 4873

Sequence ID X_DroMel_CAF1
Location 12,672,143 – 12,672,295
Length 152
Max. P 0.984251
window7954 window7955 window7956 window7957

overview

Window 4

Location 12,672,143 – 12,672,255
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 96.43
Mean single sequence MFE -31.90
Consensus MFE -30.19
Energy contribution -31.00
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.92
Structure conservation index 0.95
SVM decision value 1.97
SVM RNA-class probability 0.984251
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12672143 112 + 22224390
CCCAAAGUGCUUUGGUGUGCGUAAAGGGCCAUUGUGAUUUUAAUUUUCAUGGCUCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCU
.....((.(((((((((.((((...(((((((...(((....)))...)))))))((((((.....)))))).)))))))))))..(((((.((.....)))))))..)))) ( -31.90)
>DroSec_CAF1 25765 110 + 1
GCCAAAGUGCUUUGGUGUGCGUAAAGGACCAUUGUGAUUUUAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGC--
........(((((((((.((((...((.((((...(((....)))...)))).))((((((.....)))))).)))))))))))..(((((.((.....)))))))..))-- ( -26.40)
>DroEre_CAF1 24976 112 + 1
UCCAAAGUGCUUUGGUGUGCGUGAAGGGCCAUUGUGAUUUUAAUUUUCAUGACCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCU
.....((.(((((((((.((((((.(((...(..(((.........)))..)))).(((((.....))))))))))))))))))..(((((.((.....)))))))..)))) ( -31.50)
>DroYak_CAF1 29116 112 + 1
CCCAAAGUGCUUUGGUGUGCGUGAAGGGCCAUUGUGAUUUUAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCU
.....((.(((((((((.((((((.(((((((...(((....)))...))))))).(((((.....))))))))))))))))))..(((((.((.....)))))))..)))) ( -37.80)
>consensus
CCCAAAGUGCUUUGGUGUGCGUAAAGGGCCAUUGUGAUUUUAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCU
........(((((((((.((((((.(((((((...(((....)))...))))))).(((((.....))))))))))))))))))..(((((.((.....)))))))..)).. (-30.19 = -31.00 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,672,143 – 12,672,255
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 96.43
Mean single sequence MFE -29.40
Consensus MFE -28.75
Energy contribution -28.62
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.98
SVM decision value 1.35
SVM RNA-class probability 0.944859
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12672143 112 - 22224390
AGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGAGCCAUGAAAAUUAAAAUCACAAUGGCCCUUUACGCACACCAAAGCACUUUGGG
.((((.(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).)))).............))))...........(((((....))))). ( -29.80)
>DroSec_CAF1 25765 110 - 1
--GCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUAAAAUCACAAUGGUCCUUUACGCACACCAAAGCACUUUGGC
--..........(((..(((((.((((((((.(((((.((.((((((...)))))))).))))))))))))).........((((...........)))))))))..))).. ( -27.90)
>DroEre_CAF1 24976 112 - 1
AGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGUCAUGAAAAUUAAAAUCACAAUGGCCCUUCACGCACACCAAAGCACUUUGGA
.((((.(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).)))).............))))...........(((((....))))). ( -28.50)
>DroYak_CAF1 29116 112 - 1
AGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUAAAAUCACAAUGGCCCUUCACGCACACCAAAGCACUUUGGG
.((((.(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).)))).............))))...........(((((....))))). ( -31.40)
>consensus
AGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUAAAAUCACAAUGGCCCUUCACGCACACCAAAGCACUUUGGG
.((((.(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).)))).............))))...........(((((....))))). (-28.75 = -28.62 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,672,183 – 12,672,295
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 87.80
Mean single sequence MFE -20.50
Consensus MFE -16.20
Energy contribution -16.45
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.79
SVM decision value 0.45
SVM RNA-class probability 0.740925
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12672183 112 + 22224390
UAAUUUUCAUGGCUCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCUUGUAACCUAGUAUUAAAUGCACAUAAUUGAUUGUAUGCGG
...((((.(((((.(((((((.....))))).)).))))).)))).(((((((......(((.....))))))))))............((((.((((....)))).)))). ( -24.00)
>DroSec_CAF1 25805 99 + 1
UAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGC-------------AUUAAAUGCACAUAAUUGAUUAUAGUCGG
(((((((.(((((.(((((((.....))))).)).)))))..)))))))...(((...((((.....)))-------------).....))).......((((....)))). ( -21.20)
>DroEre_CAF1 25016 112 + 1
UAAUUUUCAUGACCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCUUGUGCCCUAGUGUUCAACGCACAUUAUUGAUUAUAUUCGU
........((((...((((((((..........((((.........(((((.((.....))))))).......))))....((((.....)))).)))))))).....)))) ( -17.69)
>DroYak_CAF1 29156 112 + 1
UAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCUCGUAACCUAGUAUUCAACGCACAUUAUUGAUUAUAUUCUU
...((((.(((((.(((((((.....))))).)).))))).)))).(((((.((.....)))))))...............(((.((((.........)))).)))...... ( -19.10)
>consensus
UAAUUUUCAUGGCCCGUCAAUAAAACAUUGAUCGCGCCAUCAAAAAUUACAAGCAAAUUGCUGUAAAAGCCUUGUAACCUAGUAUUAAACGCACAUAAUUGAUUAUAUUCGG
...((((.(((((.(((((((.....))))).)).))))).)))).(((((.((.....))))))).............................................. (-16.20 = -16.45 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,672,183 – 12,672,295
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -25.73
Consensus MFE -20.91
Energy contribution -20.73
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.81
SVM decision value 0.57
SVM RNA-class probability 0.786835
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12672183 112 - 22224390
CCGCAUACAAUCAAUUAUGUGCAUUUAAUACUAGGUUACAAGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGAGCCAUGAAAAUUA
..(((((.((....)).)))))............(((((((((((.....)))......))))))))((((.(((((.((.((((((...)))))))).))))).))))... ( -25.80)
>DroSec_CAF1 25805 99 - 1
CCGACUAUAAUCAAUUAUGUGCAUUUAAU-------------GCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUA
............(((((((.(((.....(-------------(((.....))))...))).)))))))(((.(((((.((.((((((...)))))))).))))).))).... ( -24.10)
>DroEre_CAF1 25016 112 - 1
ACGAAUAUAAUCAAUAAUGUGCGUUGAACACUAGGGCACAAGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGUCAUGAAAAUUA
.................(((((.(((.....))).)))))......(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).))))... ( -27.00)
>DroYak_CAF1 29156 112 - 1
AAGAAUAUAAUCAAUAAUGUGCGUUGAAUACUAGGUUACGAGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUA
....................((.((((((.....))).))).))..(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).))))... ( -26.00)
>consensus
ACGAAUAUAAUCAAUAAUGUGCAUUGAAUACUAGGUUACAAGGCUUUUACAGCAAUUUGCUUGUAAUUUUUGAUGGCGCGAUCAAUGUUUUAUUGACGGGCCAUGAAAAUUA
..............................................(((((((.....)).))))).((((.(((((.((.((((((...)))))))).))))).))))... (-20.91 = -20.73 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:05 2006